Reverse Dependencies of pysam

The following projects have a declared dependency on pysam:

• abeona — no summary
• aeqtl — eQTL analysis using region-based aggregation of rare variants.
• afplot — Plot allele frequencies in VCF files
• aimhii — A pipeline for mapping insertion mutants from whole genome shotgun data
• alcov — Identify frequencies of concerning mutations from aligned reads
• aldy — A tool for allelic decomposition (haplotype reconstruction) and exact genotyping of highly polymorphic and structurally variant genes
• align-trim2 — no summary
• allcools — Toolkit for single-cell DNA methylome and multiomic data analysis.
• altob — Identify frequencies of concerning mutations from aligned reads
• amplicnv — A Python3.x package for CNV detection
• amplicon-coverage-inspector — Visualization of coverage for amplicon sequencing
• amplicov — script to generate amplicon coverage plot
• Angua-Luggage — no summary
• annovar-tools — tools for ANNOVAR
• aqtest1 — please install samtools and minimap2 from bioconda(anaconda) in advance
• arancini — scATAC-seq utils
• ariba — ARIBA: Antibiotic Resistance Identification By Assembly
• asdeep — A deep-learning tool to interpret variant function by allelic imbalance.
• asTair — A tool for the analysis of bisulfite-free and base-resolution sequencing data generated with TET Assisted Pyridine borane Sequencing (TAPS), or other modified cytosine to thymine conversion methods (mCtoT). It also has some features for bisulfite sequencing data (unmodified cytosine to thymine conversion methods, CtoT).
• atactools — Tools for ATACSeq QC and Post-Processing
• ataqc — ATAqC - quality control for ATAC-seq
• atropos — trim adapters from high-throughput sequencing reads
• BABACHI — no summary
• bam_add_eof — if a BAM is missing EOF, add it, else output original BAM
• bam-filter — A simple tool to filter references from a BAM file using different filter types
• bam_readgroup_to_json — convert each readgroup id to a json file from a BAM
• bam-shot — A tools of bam to image
• bam2plot — Plot of coverage from bam file
• bam2tensor — Bam2Tensor
• bamAlignCleaner — Removes unaligned references in BAM alignment file
• bamdash — create a interactive coverage plot dashboard from bam files and add gb, vcf and bed tracks
• bammix — bammix
• bamread — Read bam files quickly into dataframes in Python
• bamrefine — A small program to mask positions that could result in a PMD artifact from a BAM file using a predefined SNP catalog
• bamsnap — A converter from .bam to .png for specific genomic region.
• baseqDrops — Processing Drop-seq, 10X(3prime) and inDrop RNA-seq dataset
• beditor — A computational workflow for designing libraries of guide RNAs for CRISPR base editing
• bellerophon — Filter reads of a minimum quality that span a junction, retaining the 5´ side of that junction
• bio-mustache — Tool to identify insertion sequences from whole-genome sequencing data.
• bioat — Bioinformatic toolkit with python
• biobookshelf — a collection of python scripts and functions for exploratory analysis of bioinformatic data in Python
• biocommons.seqrepo — Non-redundant, compressed, journalled, file-based storage for biological sequences
• bioframe — Operations and utilities for Genomic Interval Dataframes.
• biofrost — The magic bifrost bridge of bioinformatic
• biometatools — Package for meta-analysis of reads compared to features
• biometrics — Package to generate sample based biometrics.
• bonsai-prp — Pipline result processing program for the JASEN pipeline and Bonsai tool.
• bp-quant — Quantification of reads at defined positions to verify custom input sequences. Given a gene fusion or splicing junction of interest, this tool can quantify RNA-seq reads supporting the breakpoint (or splice junction) by quantifying reads that map to the breakpoint (junction reads) and read pairs that span the breakpoint (spanning pairs).
• bpnet — BPNet: toolkit to learn motif synthax from high-resolution functional genomics data using convolutional neural networks
• Broad-GenePy — A useful module for any CompBio
• BSBolt — Bisulfite Sequencing Processing Platform
• callingcardstools — A collection of objects and functions to work with calling cards sequencing tools
• camu — A package for filtering candidate mutations for spontaneous mutation rate estimates.
• candig-server — Server implementation of the CanDIG APIs
• cap2 — CAP2
• capcruncher — An end-to-end solution for processing Capture-C, Tri-C and Tiled-C data
• capfinder — A package for decoding RNA cap types
• capture-assembler — The Capture seq assembler
• catfishq — Cat FASTQ files
• CAVA — CAVA (Clinical Annotation of VAriants)
• ce-detector — A program used to detect Cryptic Exon.
• celescope — Single Cell Analysis Pipelines
• cemba-data — Pipelines for single nucleus methylome and multi-omic dataset.
• cfdna — Python package for fragment manipulation for cfDNA
• cflib-pomo — Counts file library and conversion scripts.
• chame — Chromatin accessibility module
• checkm-genome — Assess the quality of putative genome bins.
• chunked-scatter — Chunk and scatter the regions in a bed or sequence dict file
• CIRCexplorer2 — Circular RNA analysis toolkits
• circfull — circfull: a tool to detect and quantify full-length circRNA isoforms from circFL-seq
• Circle-Map — Circular DNA analysis tools
• circtools — circtools - a circular RNA toolbox
• circulocov — Circular-Aware Coverage for Draft Genomes
• CIRI-long — circular RNA identification from Nanopore
• CIRIquant — circular RNA quantification pipeline
• civicpy — CIViC variant knowledgebase analysis toolkit.
• clipoverlap — Clips overlapping regions in read mates of SAM/BAM files.
• clodius — Tile generation for big data
• clubcpg — CluBCpG is a software package built to analyze whole genome bisulfite sequencing (WGBS) data.
• CMSeq — Set of utilities on sequences and BAM files
• cnvfinder — A Python3.x package for CNV detection
• CNVkit — Copy number variation toolkit for high-throughput sequencing.
• CNVpytor — Python extension of CNVnator
• cobra-meta — COBRA (Contig Overlap Based Re-Assembly) is a bioinformatics tool to get higher quality viral genomes assembled from metagenomes of short paired-end reads. COBRA was written in Python. COBRA has so far only been tested on assembled contigs from metaSPAdes, IDBA_UD, and MEGAHIT.
• compare-reads — cythonized function to compare reads by name
• Connor — Command-line tool to deduplicate reads in bam files based on custom inline barcoding.
• cooler — Sparse binary format for genomic interaction matrices.
• coptr — Accurate and robust inference of microbial growth dynamics from metagenomic sequencing reads.
• corecomb — no summary
• corsid — Core Sequence Identifier
• counhto — Python package for generating and demultiplexing hash tag oligo count matrices from cellranger output
• count-fgs-sam — Count Functional Genomics Screen alignments in a SAM file with filtering options
• covpipe — Sars-Cov-2 NGS Pipline for generating consensus sequences
• CPAT — CPAT (Coding Potential Assessment Tool).
• CrossMap — CrossMap -- Lift over genomics coordinates between assemblies.
• cstag-cli — Command line interface of cstag to manipulate the minimap2's CS tag
• culebrONT — CulebrONT is an open-source, scalable, modular and traceable Snakemake pipeline, able to launch multiple
• cuteFC — Regenotyping structural variants through an accurate and efficient force-calling method
• cuteSV — Long-read-based human genomic structural variation detection with cuteSV
• cwas — Category-wide association study (CWAS). This is a data analytic tool to perform stringent association tests to find non-coding loci associated with autism spectrum disorder (ASD).